Microorganisms cycle nutrients in every environment on Earth, and their importance in aquatic environments has been recognized for at least 75 years. However, many systems key to better understanding the role specific microbes play in natural environments remain poorly characterized. Lake Baikal is a UNESCO world heritage site. It is the planet’s deepest (1642 m), most voluminous (23615 km3), and oldest (25 to 30 my) lake, containing about 20% of world’s unfrozen freshwater. Baikal’s size and millions of years of evolutionary development have turned this ancient system into a biodiversity hotspot; however, little is known about its microbial communities. I describe what is the first -omic based survey the microbial communities of Lake Baikal, covering all three basins, multiple depths, and including measured environmental covariates.In Chapter One, I show that temperature, stratification, nutrients, and dissolved oxygen define major microbial habitats and influenced patterns of community diversity in summer Lake Baikal. The environment, not geographical distance, structured microbial communities in Lake Baikal. The overall main driver of community dissimilarity was temperature. Increases in community diversity are driven by richness in the upper mixed layer and evenness in the deep waters, and those aspects of diversity were associated with different environmental drivers. Next, we used a co-occurrence network to identify lake habitats consistently preferred by groups of co-occurring microorganisms, discovering two sets of candidate resident and two sets of candidate transient habitat-cohort pairs. Taxonomic makeup reflected the abiotic conditions of those clusters, suggesting key microbial players in each one.In Chapter Two, I expand microbial community and functional surveys to thirteen additional lakes across Michigan, Minnesota, and Wisconsin, sampled in summer and winter seasons. Lake Baikal indeed harbored microbial communities that were distinct from other north temperate lakes in both seasons, with the next closest communities supported by oligotrophic epilimnia of lakes Superior, Portsmouth, and La Salle. In summer epilimnion of Lake Baikal, which was N-P co-limited at the time of the survey, the enzymes responsible for assimilatory reduction of N species to ammonium and assimilation of ammonium into glutamate were present in ferredoxin-dependent at the low end of N availability gradient, in a trade-off with NADH-dependent, isoforms.Chapter Three presents 369 high quality draft genomes of microorganisms from Lake Baikal, assembled using computational tools that are currently at the cutting edge of bioinformatics. The metagenome assembled genomes (MAGs) were culture-independent and included the archaea domain, as well as 15 bacterial phyla, four of which have no previously sequenced lineages from Lake Baikal. Most MAGs were small but with large variation. At the same time, genomes assembled from the most stable, aseasonal, and resource environment in the Lake Baikal hypolimnion harbored the smallest genomes with remarkably little size variation, reflecting the oligotrophic environment.
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